A resource for transcriptomic analysis in the mouse brain
Open accessAbstract
BACKGROUND: The transcriptome of the cerebral cortex is remarkably homogeneous, with variations being stronger between individuals than between areas. It is thought that due to the presence of many distinct cell types, differences within one cell population will be averaged with the noise from others. Studies of sorted cells expressing the same transgene have shown that cell populations can be distinguished according to their transcriptional profile. METHODOLOGY: We have prepared a low-redundancy set of 16,209 full-length cDNA clones which represents the transcriptome of the mouse visual cortex in its coding and non-coding aspects. Using an independent tag-based approach, CAGE, we confirmed the cortical expression of 72% of the clones. Clones were amplified by PCR and spotted on glass slides, and we interrogated the microarrays with RNA from flow-sorted fluorescent cells from the cerebral cortex of parvalbumin-egfp transgenic mice. CONCLUSIONS: We provide an annotated cDNA clone collection which is particularly suitable for transcriptomic analysis in the mouse brain. Spotting it on microarrays, we compared the transcriptome of EGFP positive and negative cells in a parvalbumin-egfp transgenic background and showed that more than 30% of clones are differentially expressed. Our clone collection will be a useful resource for the study of the transcriptome of single cell types in the cerebral cortex.
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A key target of Otx2 may be the increased ATP metabolism found in fast-spiking cells.
“An important Otx2 target may be the enriched ATP metabolism in these fast-spiking cells (Plessy et al., 2008).”
From Choroid-Plexus-Derived Otx2 Homeoprotein Constrains Adult Cortical Plasticity (2013) · cites this paper as Plessy et al., 2008
Fast-spiking PV-cells are highly metabolically active, rich in mitochondria, and especially vulnerable to redox dysregulation, leading to oxidative stress and PNN loss.
“Notably, fast-spiking PV-cells are highly metabolically active with a hallmark of abundant mitochondrial molecules (Plessy et al., 2008) and are particularly vulnerable to redox dysregulation as compared to other neuronal types, resulting in their enhanced oxidative stress and loss of PNNs (Cabungcal et al., 2013a,b).”
From Clock Genes Control Cortical Critical Period Timing (2015) · cites this paper as Plessy et al., 2008
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Lynx1, a Cholinergic Brake, Limits Plasticity in Adult Visual Cortex
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- Authors
- Plessy, C., Fagiolini, M., Wagatsuma, A., Harasawa, N., Kuji, T., Asaka-Oba, A., Kanzaki, Y., Fujishima, S., Waki, K., Nakahara, H., Hensch, T. K., & Carninci, P.
- Affiliations
- RIKEN (JP)
- RIKEN Center for Brain Science (JP)
- Corresponding author
- Hensch, Takao K.
- Carninci, Piero
- ORCID
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2008-08-20
- Volume
- 3
- Issue
- 8
- Pages
- e3012
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC2507754
- OpenAlex
- W2030594771
- Cited by
- 12
- References
- 40
- Citations by year
- 2024: 1 · 2020: 1 · 2016: 1 · 2015: 2 · 2013: 1 · 2012: 5
- FWCI
- 0.14
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Ministry of Education, Culture, Sports, Science and Technology
- Japan Society for the Promotion of Science (18020034, 17680029)
- RIKEN
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Keywords
- mouse cortex, full-length cDNA clone, cDNA microarray, cell type-specific gene expression, differential gene expression, single-cell transcriptomics, transcriptome annotation
- MeSH terms
- Animals, Brain, Cerebellum, Nerve Tissue Proteins, Transcription, Genetic, Visual Cortex, Models, Statistical, Gene Library, DNA, Complementary, Expressed Sequence Tags, Gene Expression Profiling, Mice
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